Equestria and the Time Lord Episode 5: The Greatest Power
by The Orwellian Writer
Summary: The Doctor's investigations take him to Baltimare in 1003, where he finds something much greater: the wielder of the greatest power. He's kept it secret for 4 years, but somepony else wants it now. The Doctor realizes that he must stop the new wielder from destroying everything in his mad hunger, as the story continues, or comes to an abrupt and deadly ending.
1. Prologue: Golden Death

Equestria and the Time Lord Episode 5: The Greatest Power

Prologue: Golden Death

**=Gaia, Equestria, The Badlands, The Golden Cave, 999 C.E. =**

The stalagmites hanging from the ceiling continued to drip down on to the ground repeatedly as they continued to form a small puddle on the cave floor. But what you could barely see down in that puddle was something pulsating down in the water, like it was alive…

The distant sound of a train pulling in could be heard, and then the ever growing sound of hooves galloping towards the cave. After a few minutes, a pony stuck his hooves through the narrow opening to the cave. This pony was an ordinary earth pony with a caramel colored coat, a brown mane, brown eyes, and a cutie mark of a magnifying glass looking at a yellow puzzle piece. He was wearing gold colored half-moon glasses, a heavy looking saddlebag, and he was about 17. This pony trotted up to a desk that had been set up in the middle of the room, and examined the mess of papers he had set there.

He opened up his saddlebag and began pulling out a few metal objects. He had just gone back to the main lands to get some equipment for his research. He knew it looked like just an ordinary cave, but he knew from his instincts that he would find something very interesting down here.

He pulled out a pair of tongs and carried them over to the small pool of water. He jammed it down into the water and felt around the bottom with it. He suddenly felt something down in it. He smiled as he opened the tongs and tried to get a hold on it. He knew if it turned out to be just a large rock, he would be beyond annoyed. He managed to get both ends of the tongs around the large whatever it was that was down there. He closed the tongs around it, and pulled it out.

It was a large golden colored crystalline type of object. It almost felt like there was a beating heart deep down in there.

"Well this is certainly interesting." He said to himself in a voice that sounded exactly like that which the Doctor when he regenerated into his fifth incarnation, would later have. "It's not even wet in the least."

He decided to look at it more closely as he carefully carried it over to his desk. With one hoof, he gathered up his notes and papers and jammed them into his saddlebag. He opened the tongs and the golden stone fell onto the desk. It singed the paint from the desk off of the desk. He looked at it very closely. He felt the need to look closer, even touch it, and see what it was supposed to be. He reached forward and placed his hoof on it. Immediately he was thrown back by a burst of energy, landing directly into the pool of water. He drew his head out, panting for air. He looked up to see that the stone had vanished, and his desk was on fire, burning to ashes.

He quickly pulled himself out of the water, and looked into the water as he pulled himself out. As the ripples in the water receded, he was shocked to discover that a unicorn horn had now grown out of his head. His eyes were glowing a golden color now, and the stone was partially sticking out of his chest. He looked over to the fire. His new horn glowed, and the fire went out. His eyes widened. He used the horn to levitate a coat that he had hanging on the cave wall and put it on, buttoning up the coat so that it covered over the stone in his chest.

As it all sunk in, he smiled widely and levitated his saddlebag over and put it on. His smile grew even wider. "I'm going to have some fun with this!" he said triumphantly as he went to the entrance to the cave and pulled himself out of it.

As he stepped into the desert, he didn't care any longer about the tremendous heat. He simply used his horn to change the temperature of the air around him. He knew he didn't have to care about anything anymore.

**=Place Unknown, Year, Date, and Time Unknown =**

Daring Do rubbed her head in pain, no wait, she didn't know what she was feeling, as she came back to consciousness and her surroundings became clearer around her.

She could see that she was sitting inside of what looked like a cave. Yes, it certainly seemed like she was sitting inside a rather small cave. She looked around the cave. She was completely alone in the cave… except for that other pony.

It was the caramel coated unicorn, with his eyes glowing gold, sitting with a black cloth wrapped around his body. She didn't know who he was. It sort of felt like she knew who he was, but she didn't know who he was. So, she decided to ask.

"Who are you?" she asked him.

The pony looked at her. "You don't remember? Well, I suppose having your mind harvested and used to feed an evil monster would have debilitating affects on your memories. Oh, where have my manners gone? Hello, my name is Puzzlehunt." The stallion said.

Another question came to her mind. "Alright Puzzlehunt, do you know where the Doctor and Romana are?"

Puzzlehunt wouldn't answer that one.

She rubbed her head. "Ugh, I feel so weird. One more. What happened, how did I get here, and how do you fit into this?" she asked.

Puzzlehunt simply looked out of the mouth of the cave and into the landscape below.

Daring Do got up and hobbled over. She also looked out into the landscape below. Horror filled her mind as she gasped.

Outside the cave were the ruined remains of a city. Buildings were smashed and completely broken down to the ground. The same had happened with smaller houses. Dried cracks had had been burned into the ground. The whole place was nothing but smashed rubble. The bodies of ponies were lying down all over the ground through that smashed rubble. She looked at the outside of the cave to see that they were not sitting in a cave, but the charred remains of a room in what looked to be the only still standing building in the city. The whole place was echoing with terrifying death all over, and there was nothing to say that this wasn't what the rest of the world was like as well.

Daring Do felt her heart race and her hooves wobble as she tried to take this all in.

"Well." Puzzlehunt said darkly. "It's a very long story."


	2. Chapter 1: The Wall of Lies

Chapter 1: The Wall of Lies

"Well, it all started about 3 days ago. Everypony was minding their own business, when, without notice…"

**=Gaia, Equestria, Baltimare, Just Outside the Archeological Institute, 1003 C.E. =**

The TARDIS began to materialize at the edge of the street, surprisingly going unnoticed by anypony nearby. The Doctor stepped out of it, looking around the semi-high semi-low buildings. Not as big as Canterlot, but still reasonably larger than some cities. Daring Do followed shortly after, examining the place. The Doctor walked in and walked over to K9. "Won't be needing you this time, K9."

"Master?" K9 said.

"No, we haven't been needing you much at all lately. See you." The Doctor said.

Romana sighed as the Doctor walked back out. She followed suit shortly after.

"So what year is it this time?" Daring Do asked as she looked around the city.

"1003 C.E." The Doctor told her.

"Again?" Daring Do asked.

They walked around the city for a few moments before Romana felt the need to ask something.

"Doctor, you never really told us why you were interested in coming here." She said seriously.

"I was simply interested in seeing a nice city where we won't end up on the Moon." The Doctor said, feigning astonishment. "Nothing here that I want to investigate." He finished as he secretly pulled out the page that he got from a newspaper that he got from a device that detects things worth investigating and reread it.

_**The Baltimare Times**_

_January 7, 1003 C.E. _

_The citizens of Baltimare are still baffled by random holes in memory in Everypony in town over the last four years. Nopony has been able to figure out the cause, and there have been some reports of the same case in random areas all over Equestria, but they are most concentrated in this city. Another oddity throughout the city is high levels of energy concentration all over the place. Answers still continue to be lost._

That article was published yesterday. They would have to be somewhere near the source of all this amnesia and energy. He put the article back into his pocket and continued walking. He wondered how long it would take to find it.

Almost immediately, somepony else bumped into him. This pony had a caramel coat; a brown mane, golden colored eyes, was a unicorn, and was wearing a coat that obscured his chest and his cutie mark. He figured this would be normal in January, though.

"Sorry about that." The pony said, obviously quite tired.

The Doctor just looked at him. His Time Lord senses were tingling. Okay, so he didn't have Time Lord senses, but it was certainly something to that effect.

The pony however, looked directly at the TARDIS. So far, nopony else had noticed the TARDIS. They just walked right by like nothing was there at all. A few ponies had even bumped into it, but hadn't seen anything at all.

'_I got you now._' The Doctor thought as he smiled.

"There you are!" said a cruel sounding voice. The pony shivered involuntarily as he looked up to see the source of the voice, who he obviously knew.

It was an earth pony with a black coat, a neatly combed black mane, and a cutie mark of three silver colored question marks. "I knew I would run into you somewhere along the way, brother." He said that last word with sort of a hateful tone. "I came to let you know: you have **work** to be getting back to."

The pony, who you may have guessed by now to be Puzzlehunt, sighed tiredly. "I'm going to the site right now to finish the work, Mystery."

Puzzlehunt walked off, as Mystery shouted over to him: "You must remember, I am your boss!" The Doctor immediately knew he did not care to know this pony any further that he already did.

As Mystery walked away to a four-story building, Daring Do read the name on top as her eyes widened in glee. "Baltimare Archeological Institute? The sounds quite wonderful! I have always wondered what archeology would become in the future! Who knows, maybe I'll find out how I'm remembered in the future!" she said in an enthusiastic yet subdued voice so as not to give away how exited she actually was.

The Doctor and Romana wore a nervous face. They knew full well how she was remembered in the future, and it would not be happy for her if she found out. "As much as I would love to show you, knowledge of the future could blow holes in the space time continuum big enough to swallow a good amount of the universe. Say, why don't we see what the pony we just ran in to is doing wherever he is working. You could get into a futuristic archeological discovery!"

"That would be great for you!" Romana said, playing along with the Doctor's little charade.

"That would be pretty great, but how do we find out where he's working at without checking in the institute?"

The Doctor slapped his forehead. He could not believe he hadn't thought of that one. He looked a Romana to see if she had any ideas at all.

"I don't know, perhaps he'll be kind enough to tell us on his way back. In the meantime, have you ever been on a train ride of any sort?" Romana said.

"Nope. Never." Daring Do replied.

"Let's go then!" Romana said as they all walked away.

**=Gaia, Equestria, The Dead Pool, Puzzlehunt's Work Station, 1003 C.E. =**

Puzzlehunt looked at the dark green waters of the pool beneath him. He took one of his spare quills and dipped it into the water. When he pulled it out, it was all burned away. He walked over to a worktable that was identical to table he had set up when he had found… well, he didn't exactly have a name for it, but it was pretty darn cool!

He began to write down some notes**, **dictating to himself as he wrote. "This pool, nicknamed by some as the Dead Pool due to its incredibly toxic qualities to non organic life, is believed by some to be the source of the transformative powers of the Changelings. Wow I do such amazing work here." He said rather arrogantly to himself as he stopped writing for a moment. He stopped dead in his tracks when he saw something while looking around his other notes.

It was a folder full of pictures taken of one thing at many different archeological sites: A blue box with the words _POLICE PUBLIC CALL BOX _written on the top of every side. And he then remembered where he had seen it before: Right next to those three ponies he had run into.

"Oh you have got to be kidding me." He said to himself as he grabbed the folder. His horn glowed as located the three. He then took off at top speed in their direction.

**=Gaia, Equestria, Baltimare, Baltimare Train Station, 1003 C.E. =**

The Doctor, Daring Do, and Romana were still waiting in the somewhat lengthy line to get on the train. There were a lot of ponies in front of them, and they could tell it would take a while.

All of a sudden, Puzzlehunt appeared right next to them. Apparently he had arrived with the force to knock a few ponies over to the other side of the tracks. Everypony in the room looked at him in shock. There was a golden light glowing from a spot behind his coat. But what was even more unusual…

"Uh, sir…" Romana began.

"Uh, my name is Puzzlehunt." He said dismissively and slightly mockingly.

"Puzzlehunt." The Doctor rebegan. "Does it bother you at all that your horn has disappeared and you grew wings?"

Puzzlehunt looked down at his Pegasus wings. "Should it?" he said uncaringly.

**=Gaia, Equestria, Baltimare, Baltimare Archeological Institute, 1003 C.E. =**

Mystery locked the door to his office and made certain no one could see inside by pulling down all the blinds. He sat down and looked over a wall. This wall had every discovery that he was known for making: And Puzzlehunt had made all of them.

He smiled at this. Sometimes most thought that he only smiled at things that made others frown and shiver. Some thought that he reveled in suffering. They were all right.


	3. Chapter 2: The Traitors

Chapter 2: The Traitors

**=Gaia, Equestria, Baltimare, Baltimare Train Station, 1003 C.E. =**

Daring Do sighed as she watched Puzzlehunt's Pegasus wings recede into his body and his unicorn horn grow back. '_Why can't anything not completely life threatening and deadly happen whenever we go somewhere? I'm used to danger, but I just know that once again, this will lead to something bad._' She sighed mentally and waited for whatever would happen next.

Puzzlehunt looked at all the many other ponies nearby that were looking at him in total shock. "And what are you all looking at?" He said as he waved his hoof over the crowd and they all fell asleep. He turned to the Doctor. "None of them will remember seeing me at all. As usual."

"Do you really think of treating other ponies memories as pieces of paper that can have bits of it torn off is ethical in the least?" The Doctor said unhappily.

"After 3 and a half years of already doing it, the word ethical is more of a limiting factor than a word with a definition." Puzzlehunt said, obviously not considering the question to be anything important. "Never mind, it has no importance. Average days and clockwork actions do not get in my way. I need to talk to you. Unlike your current interests, this is quite important."

Romana suddenly found it more believable that the pony who had passed by was his brother.

"Now wait just a minute! You can't drag us away from what we were doing! We were doing something quite-" Daring Do stopped talking when he realized they were now standing in the middle of a building. "Oh."

"Now, let me show you what I'm talking about. This would be a quite an archeological discovery if I can get it proven and not have it snatched up and taken credit for before I can do anything about it." Puzzlehunt said as he started pulling the folder out.

"Does that happen to you often?" The Doctor asked.

"Yes. My wonderful brother also decided that this closet would be a great space for my office, and gave me the most _brilliant_ reputation in the archeological community. Isn't he just great?" Puzzlehunt said in a voice that reached the Top 10 of most sarcasm the Doctor had ever heard.

The Doctor and Romana could suddenly think of a few reasons for why this pony was so arrogant.

"So you're an archeologist, hmmm? That's nice. I'm an archeologist myself, actually." Daring do told him.

Puzzlehunt turned around and looked at her more closely. His eyes widened in realization. "No way." He said in shock.

The Doctor and Romana's eyes widened as they realized what he had just realized.

"You're Daring Do!" Puzzlehunt said.

"Really? I hadn't noticed. Have you heard of me before?" Daring Do asked.

"Of course I have! Everyone here has! Although, I am surprised by your presence here" Puzzlehunt, suddenly trying to wind down his surprise, as it wasn't an emotion he showed often.

"Why so?" Daring Do asked.

The Doctor made a slashing motion across his neck to get him to shut up, but either they didn't have that signal on this planet, or he just wasn't paying attention.

"Oh I couldn't possibly think of a reason, except you're just a fictional character from a book published almost 90 years ago!" Puzzlehunt said, restarting the use of his sarcasm.

The Doctor slapped his forehead in preparation for what was going to happen immediately after.

"I'm sorry, what?" Daring Do said, slightly taken aback by this. "Just, what?"

"She didn't know, did she?" Puzzlehunt asked as he turned to The Doctor and Romana.

"She didn't." Romana confirmed.

"Would you say that she is not going to react well to this?"

"Probably not."

"I see then. Do you think we should just walk out of the room until she processes this?" Puzzlehunt asked.

The Doctor briefly saw a dash of green next to the door. He had an idea who it belonged to, but he wanted to confirm. "Before we do, do you know anyone with green eyes?"

"My brother's eyes are green. Which is why I'm not a fan of green." Puzzlehunt answered.

"I see. Could you tell us about how you changed from a unicorn to a Pegasus?" The Doctor asked.

Puzzlehunt pulled off his coat, revealing the golden crystal. "It's this, actually. It seems to be an incredibly powerful source of magic, and I haven't found a limit to its uses yet."

The Doctor was tempted to bring up his 'there is absolutely no such thing as magic' speech, but he decided not to waste time. "That's impressive."

"Yes I am." Puzzlehunt said arrogantly and far too overconfidently, pretending to have misheard what he had just said to him.

Romana rolled her eyes.

Puzzlehunt opened the door to the office, only to suddenly find the stone sieved by a pair of metal tongs.

Mystery, who had been listening at the door the entire time, pulled it out, not caring in the least if he hurt the person using it, his brother. "Thank you for that." He said evilly, as he ran away.

Puzzlehunt staggered back, but found that although his horn that he had grown attached was gone, the place in his chest where the stone had been wasn't wounded at all. "Well that was surprisingly less painful than I had expected."

Romana came up to him. "Do you think it will attach to him like it did to you?" she asked.

"It only did to me when I touched it." Puzzlehunt said.

Mystery stuck his head into the door. "You really must stop saying things out loud, brother!" he yelled out as he caught the crystal in his two hooves.

Suddenly there was a white flash that consumed everything around them. When it cleared, Mystery had disappeared.

"What was that?" The Doctor asked.

"Random teleportation. Strange, that never happened to me. There's no telling here he disappeared to. But now he has all that power, and he could be anywhere." Puzzlehunt said grimly.

**=Gaia, Equestria, The Cave of the Dead Pool, The Dead Pool, 1003 C.E. =**

The white flash receded as Mystery appeared just at the edge of the pool. With no energy to support himself, he fell into the pool.

There was no telling what the result would be. The pool gave transformative powers to all living things, but it was highly toxic to nonorganic things. And since an organic object and a nonorganic object were joined together, there was no possible way of knowing what could be happening down there. The pool rippled and bubbled.

After a few minutes, a pair of green flashing lights in the shape of eyes appeared under the thick unclear water. And then something, not somepony anymore, but something, began to rise out of the water.


	4. Chapter 3: The Enemy of the World

Chapter 3: The Enemy of the World

**=Gaia, Equestria, Baltimare, All Ponies Diner, 1003 C.E. =**

The door to the diner opened and a black coated pony with a black colored mane and the most acute green eyes came in. He sat down at an empty table and waited in the line to be served.

It was Mystery. He was covering that powerful stone with a coat similar to the one that his brother had once used. He had used his new found shape shifting powers to take his own form. He felt…odd. Like his stomach was being emptied out to make room for more and more. But wasn't hungry for that old solid food. He had left that behind. Or rather, the stone had left that behind for him. It wanted to feed, and it had given that need to him to ensure that the feeding would take place. And who was he to deny it? It wouldn't let him go. And so, he must feed.

A brown mare with curly blond hair tied up into a bun who had blue eyes and was wearing an apron that covered over her cutie mark approached hm. "Hello. Welcome to the All Ponies Diner. What would you like to order?" she asked.

Mystery smiled and looked at her. "This is going to sound like a terribly cheesy joke, no, horrendously cheesy, but I would actually like _all ponies_."

Before the waitress could laugh, he made his smile wider, revealing razor sharp teeth that looked like he intended to eat her. She tried to scream, but couldn't make a sound out of pure fear. She couldn't even move.

Green tendril like vines of energy came out of Mystery's mouth and touched her. It was very efficient and quick. Within a few seconds, the waitress had aged into a skeleton, which fell onto the ground and smashed to pieces, most of which crumbled into dust.

And of course, Everypony in the diner saw this act of malice. They all screamed and tried to rush out the door and run for their lives. Mystery suddenly remembered what Puzzlehunt had used the stone for. He waved his hoof over the fleeing crowd, and they all stopped dead as they fell into a hypnotic trance. Mystery sighed.

"Sooner or later I'll find an easier way to get my food, but for now…I must feed!" he advanced on the ponies and prepared to feed. He smiled and bared his fangs of fear.

**=Gaia, Equestria, Baltimare, Just Outside of the Baltimare Archeological Institute, 1003 C.E. =**

Puzzlehunt frowned in anger as he walked out the door of the building where he worked. "This is ridiculous! In the time it took us the calm Daring Do down and walk down three flights of stairs and out the door, who knows what Mystery has been doing with all that power he jus got! I swear, I don't have time for these useless impediments!"

"You mean walking?" Daring Do asked, slightly tired of the way this stallion acted.

"Yes! That's exactly it!" Puzzlehunt replied.

"Do you even know what he'll be doing with all that power?" Romana asked after a sigh.

"As a matter of fact, no I do not." Puzzlehunt replied. "Power can make you completely unpredictable!"

"But you are an obvious exception to that rule." Daring Do said sarcastically, rolling her eyes.

"Why yes, I am. Thank you for noticing my almost obscenely amazing precision under such pressure." Puzzlehunt said, pretending to have not gotten the sarcasm.

'_With all of his arrogance, I haven't even been able to make a remark about how well I fly the TARDIS._' The Doctor thought to himself. "Well, what do you think we should use for clues for clues to his location?" He asked out loud.

Puzzlehunt felt a metaphorical mid-1800's style light bulb go on over his head. "I have an idea!" he said as he rushed into the building and came out a few minutes later with a few pieces of paper. "I found this while I was checking out one of the many archeological sites have explored and conquered over my extensive work across Equestria. It writes down something at the exact time the thing is being written down. We could use it to see if any early news reports for tomorrow's paper about something he did is being written down about now."

"I'm pretty sure he wouldn't be at the scene of the crime to tell the reporters 'I'm the one who did it! It was me!' And so, there wouldn't be a mention of his name." The Doctor said.

"I think I can figure it out." Puzzlehunt said as he set the paper up. "I'll let you know if I can find anything."

Words began appearing on the paper. _Investigations of the murders at the One Ponies Diner have heralded tha-_ The words came to an end and a blood splatter went over part of the page.

"Uh, I think I found him!" Puzzlehunt called out to the others.

**=Gaia, Equestria, Baltimare, Just Outside the All Ponies Diner, 1003 C.E. =**

Mystery smiled as he looked over the feeding that had just taken place with all the reporters that had come to investigate the deaths that he had just made take place. It wasn't quite as appetizing as the rest to feed off that dying body, but it was necessary to spur the life in all the others to make them more appetizing.

He then knew that he couldn't be satisfied. Ever. And he couldn't even attempt to be satisfied the way he was going. He was only going a few ponies at a time, here and there. He needed to think of a way to take the whole planet's ponies. He had killed the reporters to buy himself some more time. He wasn't interested in going public yet. He would not scream of his existence to Everypony in the world until he could do it himself. He wondered where he would go next. He was hungry. He would always be hungry no matter what.

As he teleported, he thought of a more efficient system of eating. If he could eat different parts of a pony at a time, it would be more filling. He wondered about the other part of his problem. He knew he could shape-shift now, but what form would suit his means of covering the planet. In between places, his eyes widened. In between places, his lips curled into a sadistic smile.

A dark cloud began to roll over the horizon. It flashed green lightning menacingly as it began to do what it wanted to do. It grew continuously as it began covering everything.


	5. Chapter 4: The Green Death

Chapter 4: The Green Death

**=Gaia, Equestria, Baltimare, Just Outside the Baltimare Archeological Institute, 1003 C.E. =**

When Puzzlehunt saw a small storm cloud appear directly above the building where he worked, he didn't think it was just a coincidence. When the cloud began to grow menacingly and flash green colored lightning, he almost certainly knew where said cloud had come from. He walked over to the Doctor, Romana, and Daring Do. "Did you just figure out what I just figured out?" he asked them.

"It seems pretty obvious to me." The Doctor noted.

"Well, what do you think we should do?" Daring Do asked.

"Not sure. It's fascinating that his atoms haven't dispersed in that gaseous cloud form." The Doctor said.

"It looks like his source of holds him together at the same time as dispersing him." Puzzlehunt said.

"That doesn't entirely make sense." Daring Do told him.

"Neither does the Doctor sometimes, but you still listen to him and nod your head." Puzzlehunt said cynically.

Daring Do couldn't think of a way to argue with that.

"At the rate he's going at, he must mean to cover the whole planet." Romana pointed out. "Do you think the TARDIS will be safe enough to withstand?"

"Certainly." The Doctor said as they all rushed to where they knew the TARDIS was.

When they got there, they found it was gone. They realized Mystery must have lifted it up into the cloud.

"Well that looks like it will work great." Puzzlehunt said sarcastically.

"Do you have any real suggestions?" Romana said, wondering if anything could make this pony snap to another attitude.

"How about we wait it out in his office? He may be crazier than he is normally, but he isn't likely to destroy his own office. At least, not for a while." Puzzlehunt suggested.

With no better option, they ran for the building and darted through the door, running up four flights of stairs to reach Mystery's office. They quickly ran into it.

"We're the only one's in this building." Romana pointed out.

With nothing else really left to do until they could think of a plan, they looked out a window to see how this was all playing out outside.

The Pegasus of the city were confused. Well, everypony was pretty confused, but the pegasi were the most of all confused. They had never scheduled for a thundercloud to roll through the city today! And so, all the weather ponies flew up to do their duty: Disintegrate the cloud.

This, of course, turned out to be a really big mistake. When they touched the cloud, lightning that made no thunder hit them, and they crashed to the ground. Frightened, the unicorns walked over and examined them. They quickly found what was wrong with them. Their entire bodies were just fine, but their minds were just…gone. Absorbed. Taken away. Every single one of them.

Despite the terrible circumstances, Daring Do couldn't help but wonder if The Doctor would react the same way to pegasi believing they cold control the weather to unicorns thinking they could do magic.

After the weather pegasi all had been fed upon, their friends on the ground were mad. They tried to do something to stop the cloud. It pretty much ignored every move they made against it. After a few minutes, it reached down its green lightning and struck everypony there was. And if any of them tried to run or fly away, they suddenly stopped in their tracks as they were hit by the lightning. In less than five minutes, the cloud had gotten everypony in the entire city.

And then it, _he_, spoke in a booming voice that was still easily recognizable. "You are very clever, brother. I am not yet desperate enough to destroy my own office, as you said. But will come to that soon enough. The cloud will cover the planet, and then I will return here. You must **all** die eventually."

The Doctor looked to where the cloud hadn't covered yet, but found that it had covered as far as his eyes could see. Everything became darker, and he lamented that there would no longer be any time to panic. It would take them all soon enough. This was on too massive a scale to stop. He needed to find out where in that cloud was that stone that he got all his power from. But for now, he just had to wait. Soon, the time would come when they could come out. But not now.

**=Gaia, Equestria, Canterlot, Canterlot Royal Palace, 1003 C.E. =**

You must understand, Baltimare is on the East end of Equestria, so most of the cloud went out over the sea before it went over the rest of Equestria. It only hit small cities like Dodge Junction and bigger cities like Fillydelphia before it hit Equestria's capitol city. But eventually, it did.

The Royal sisters, Princess Celestia and Princess Luna, hadn't even heard of the cloud that was moving across Equestria when it hit them. It suddenly came to their attention, though, when the place followed the same pattern that every city that it had come to. Weather ponies try to bust it, got their minds eaten, makes the unicorns fire all that they've got at it, spurs a panic in the streets, eats the minds of all of them.

And so the Royal Sisters realized that all of Canterlot had gone silent around them. They flew up to the cloud. "Monster!" Luna shouted. "We shall not let you best us!"

Needless to say, it did.

**=Gaia, Equestria, Ponyville, Ponyville Park, 1003 C.E. =**

Princess Twilight Sparkle was having a very ordinary picnic with her friends. She may have been a princess with very responsible duties, but that didn't stop her from having a bit of ordinary pony fun with her best friends in the entire world.

All of a sudden, a dark cloud rolled over them and darkened everything around them. Rainbow Dash looked confused. "There wasn't any thunderstorm scheduled for today!" she told her friends. "Hold on, I'll go up and bust it." She flew up to the cloud.

"Rainbow, wait!" Twilight said, having this terrible feeling.

But it was too late. Just before Rainbow Dash was hit by the lightning and struck down, she could hear a voice rumble zealously "This is too easy." And then it hit her and everything was gone.

Twilight couldn't speak. She could feel her eyes well up with tears. This was one of her best friends in the world, now just gone. Anger mixed in with her sadness as she stood up to take action against the cloud.

But there was no time to take action. The green lightning came down to everypony. One of the last things Twilight heard was evil laughter and the screams of her friends.

**=Gaia, Equestria, Baltimare, Baltimare Archeological Institute, Mystery's Office, 1003 C.E. =**

Romana could suddenly just feel it. Like millions of screams at once dying out at once or something like that. "He's done it. He covered the entire world. He got everypony." She said grimly.

"That wasn't even a single hour." Puzzlehunt said.

Then, before another word was said, more of the lightning came down, but this time there was thunder. It zapped everything into rubble. Before they knew it, everything except the building they were in was rubble. They were in the middle of a wasteland.

And then the ponies stood up. They crawled out of the rubble and stood up. Their bodies without a mind were now being moved like puppets on a string.

And then they walked. They came to the door of the building. They pounded and pounded on it. They burst through the door and swarmed into the building.


	6. Chapter 5: Horse of Destruction

Chapter 5: Horse of Destruction

**=Gaia, Equestria, Baltimare, Baltimare Archeological Institute, Mystery's Office, 1003 C.E. =**

"You know, I don't think this qualifies as a bad thing at all!" Puzzlehunt said sarcastically as the ponies began to rage into the building.

"Really? Now?" Daring Do said. "Does anypony have a plan at all?"

"One that may well not work, but yes, I have something of a plan." The Doctor said as without anther word, he opened the door to the room and walked out.

The others looked at each other and followed him.

The Doctor looked around the top floor repeatedly until he found what he was looking for: the stairs to the roof. He opened the door to it and began to climb up. The others went in and closed the door behind them, as they remembered that all the ponies that had their bodies being used didn't seem to be able to use doorknobs.

They climbed until they reached the roof. The cloud was only a foot above their heads. The Doctor pulled out his sonic screwdriver. He turned it on. It began to cut a hole in the cloud.

"You understand that only Pegasi can walk on clouds, right?" Daring Do pointed out.

"You understand that this isn't exactly a cloud, right?" The Doctor counterpointed out. "Hopefully, the compression at the same time of the dispersal will keep it compressed enough to stand on." He finished the hole, jumped up, and began to pull himself up. When he got on top of the cloud and realized he wasn't falling through, he motioned for the others to come up as well. Once Romana, Puzzlehunt, and Daring Do had gotten their way up there, The Doctor used the sonic screwdriver to seal up the hole.

"There we are!" He said.

"So what do we do now?" Puzzlehunt asked impatiently.

"Well, the power source of Mystery and the cloud form he inhabits would have to be somewhere in the epicenter of its spread: Baltimare." The Doctor explained.

"So we would just need to cut a circle around Baltimare, and the rest of the cloud will disintegrate, and then we just cut smaller circles until we find the source." Romana finished for him. "Puzzlehunt, would you know where the city limits are?"

Puzzlehunt sighed. "I'll lead the way." He walked away, with the other three following him.

**=Gaia, Equestria, The Cloud Hanging Above the Planet, Mystery's Innermost Thoughts, 1003 C.E =**

Mystery thought about the next stage of his feeding and when it took place. He would consume the bodies of the ponies whose minds had been eaten. His brother wasn't fit to stop him. He couldn't stop him. There was no way. He now knew every single thing that his food once knew. He knew everything in living knowledge on his whole planet and soon he would very soon move on to more. Nothing could satisfy him. He would take whatever he wanted as he now had the means to do so. He didn't care about others anymore. He must feed!

**=Gaia, Equestria, The Cloud Hanging Above the Planet, At the Edge of Baltimare's City Limits, 1003 C.E. =**

Puzzlehunt came to a stopas he tried to draw a line in the cloud with his hoof as best as he could. "It should be about here." He said.

The Doctor came forward and began cutting on that line with his sonic screwdriver. "Now we just need to do this across the entire city."

"This won't take long at all." Puzzlehunt said sarcastically. "It'll be so incredibly easy to do, don't you think?"

"Will you cut that out?" Daring Do said, obviously very annoyed.

The Doctor continued on his way as he cut the circle into the cloud. The only problem they would have now is keeping on track the whole way around the city. "I'm trusting you to keep us on the correct path." He said to Puzzlehunt, who nodded.

They kept moving forward. They knew full well that this could take quite while, but they kept going forward.

**=Gaia, Equestria, The Cloud Hanging Over the Planet, Mystery's Innermost Thoughts, 1003 C.E. =**

Mystery's anger increased. He was actually feeling physical pain at the cutting through his cloud body, even though he didn't exactly have a physical body. He felt the need to destroy them all then and there. He was in control of everything, yet they still felt the need to try and stop him! He took a deep mental breath. No. Underestimating your enemies was how most villains ended up defeated. And he fully accepted that he was the bad guy in this situation. He didn't care in the least about that. But what he did care about was to feed. Hunger had replaced all other drives he had. He wouldn't underestimate his brother, or even more, The Doctor, but he wouldn't overestimate them either. They would not stop him. He would kill them first.

**=Gaia, Equestria, The Cloud Hanging Over the Planet, At the Edge of Baltimare's City Limits, 1003 C.E. =**

Daring Do couldn't help but feel a twinge of wonder. The whole planet, covered in this perfect cloud. It was a sight unlike anything she had seen before, and she had seen a lot of stuff before. In a completely twisted way, it was quite beautiful. It looked really wonderful in its own sense.

"Okay, we're almost there!" The Doctor cried out to his friends (And Puzzlehunt, who he wasn't quite sure about yet.)

That was true. They were about a foot from cutting the city off the rest of the cloud. The Doctor moved it inch-by-inch over 12 inches. In only a few seconds, they had gotten through and they watched what happened to the rest of the cloud.

The rest of the cloud began to drift away from the part of the cloud over the city that they had cut off. It grew less and less clumped together as it drifted away, with holes appearing in it as it turned from a dark color to a white color. More and more hole appeared in it, until it was more sky than not. By the time it was finished, it was only a few small clouds here and there.

"Do you think that will give back the minds to the ponies living in the rest of the world?" Daring Do asked him.

"Oh, not even close." The Doctor said. "But we will be that much closer to helping them."

Then, the cloud (Mystery) began to flash menacing green lightning.

"What this time?" Daring Do asked herself.

The flash went everywhere, and when it finally died down, The Doctor and Romana had completely disappeared without a trace.


	7. Chapter 6: Mission to the Unknown

Chapter 6: Mission to the Unknown

**=Outer Space, 4500 Miles Above in Orbit Above the Planet Gaia, The TARDIS, 1003 C.E. =**

The Doctor and Romana reappeared. They looked around to see where they had teleported to. They realized they were in the TARDIS console room. The Doctor walked over to K9.

"K9. Do you know where the TARDIS is right now?" he asked him.

"Insufficient data, Master." K9 told him.

The Doctor sighed. "Thanks a lot, K9." He said as he walked over to turn on the scanner.

"'Thanks a lot' is a non computational statement as I did not do anything that helped you, Master." K9 corrected.

The Doctor tried to press the scanner button, but found it was not working. He walked over to the doors. "Looks like I'll have to do it the old fashioned way." He muttered to himself. He threw open the doors.

Immediately he could feel all the air rushing out, as the oxygen field wasn't engaged. He closed the doors quickly after just enough time to see that…

"We're in space." He told Romana.

"And I'm guessing all the systems are jammed, correct?" she asked him.

"True. It looks like all we can do until the systems aren't being jammed is sit here being useless." The Doctor said rather sadly.

"Not true. We can still devise some sort of way to fly or at least move the TARDIS a little from here." Romana said.

And with that, they stood up and went to try something to get the TARDIS going.

**=Gaia, Equestria, The Cloud Hanging Above Baltimare, On the Edge of the City Limits, 1003 C.E. =**

Daring Do and Puzzlehunt barely had any time to process the Doctor and Romana's disappearance before the cloud they were standing on became transparent…and intangible.

As they fell through it, the managed to redirect their fall onto a building top. Not that it was that hard, because the cloud was basically right over their heads from that building top. After standing up, Puzzlehunt walked over and found something.

"The sonic screwdriver." He said as he picked it up. He held it up and pressed the button. A whirring noise came out as the cloud above him smoked. "It still works too!"

"We can still use it to cut the cloud and find the source, then!" Daring Do said.

After a brief moment of figuring out how to use it, Puzzlehunt went to the other side of the roof top and began cutting through the cloud. "We'll just do it from under here on the roof tops and avoid all the mind-locked ponies down there. With me using the screwdriver, this should really be easy!"

Daring Do rolled her eyes, but followed him as he cut along the ceiling of the cloud/ Mystery. When they got to the edge of the roof top, he motioned for motioned for her to lift him up. She did so after an eye roll, a kept along the same path, holding him up long enough to get through the not very thick cloud. Then she set him down on another roof top. And then she realized this would probably be harder than it looked originally. She decided to put up with it, though.

**=Gaia, Equestria, The Cloud Hanging Above Baltimare, Mystery's Inner Thoughts, 1003 C.E. =**

Hmm. They are working forward. But I don't care. I essentially control everything there is. I let them move forward for they will never move far enough to get to my power source. I refuse to let them. They will go on a little bit longer. Keep cutting your circles. When I bring forth intervention, it will become a futile effort not worth pursuing. They will all diiiiiiieeee… Puzzlehunt will die…

**=Gaia, Equestria, Baltimare, The Rooftops under the Cloud, 1003 C.E. =**

Puzzlehunt finally used the sonic screwdriver to cut through that last foot of cloud in that circle. He made a motion again, and Daring Do sprang up and kicked the circle off of the rest of the cloud. It floated off and dissipatated just like the other bit of the cloud did. Puzzlehunt held up the sonic screwdriver and activated it, but the whirring sound stopped. "Oh no."

"What is it?" Daring Do asked.

"Well, I'm no expert on this kind of technology, but apparently, this is almost out of battery life." Puzzlehunt said.

"How much do we have left?" Daring Do asked him.

"About enough to make one guess as to were the power source is, point there, and click." Puzzlehunt said in annoyance." I swear, this thing is so…" he didn't finish. "What are we going to do now?"

"We could go back to your work. It seems like the best place to make a guess from." Daring Do noted.

"Good idea." And then they went down through a door from the roof into the building.

They descended from floor to floor, making sure there were none of the controlled ponies nearby. When they found none on the floor they were on, they sighed in relief and opened the door to the stairs. They jumped back at least a foot to see a controlled pony coming towards them.

"Really?" Puzzlehunt said to himself angrily.

They jumped over it. Due to all brain functions being gone, it needed to wait until Mystery, the controller, registered them as being behind him before he could move.

Meanwhile, Puzzlehunt and Daring Do were hiding behind a bush, only about 25 feet from the entrance to the Baltimare Archeological Institute. "Wouldn't it have been easier to go across the rooftops again?" Daring Do asked him.

"You waited until now to tell me this?" Puzzlehunt yelled at her. Then he realized how loud he had said that.

When the controlled ponies started coming for them, they made a run for it, bursting through the door of the Institute and barricading it.

"Don't you think that we might have barricaded ourselves in here with several controlled ponies?" Daring Do asked him.

Puzzlehunt slapped his forehead.

They walked up the stairs and walked around as carefully as physically possible so as to avoid more of the controlled ponies.

When they got up to the fourth floor, they went into it and found at least a dozen controlled ponies. None of them, however, were inside of Mystery's office. They stalked around, trying to find a way to get in to the office. They moved from hiding place to hiding place, until they accidentally came out into the open.

To their surprise, none of the controlled ponies came towards them. So, they cautiously moved to the office, opened the door, and went inside.

And then, all of a sudden, the office was incinerated. A fireball burned off the walls, incinerated all the furniture and papers, and turned one wall completely to ash. The office looked more like a cave than an office. The form of Mystery came down in front of them, riding on a tornado like funnel. "If you're wondering, I am that desperate now."

Green tendril like vines of energy grabbed both of them. "But this time, I will take no chances."

Puzzlehunt felt his body disappear. He was being completely consumed, mind and body. Evil laughter filled his ears as total death began to set into him. He could hear the scream of Daring Do next to him before everything turned into a blur.


	8. Chapter 7: War of God

Chapter 7: War of God

**=Gaia, Equestria, Baltimare, Baltimare Archeological Institute, Mystery's Office, 1003 C.E. =**

Puzzlehunt needed to get away. With the Doctor having been teleported to wherever he was, if he were gotten here (as Mystery was feeding on Daring Do and was saving him for the very last.) there wouldn't be anypony to stop him from moving through the universe and leaving it a barren lifeless place, and wasn't likely that he would try to stop there. He looked for any opening at all to get out of this before it was too late for that. Then he saw a small one, one that just might work.

Mystery finished with Daring Do and turned to Puzzlehunt to prepare to finish this planet that he put up with for nearly 25 years. "Well what can you possibly do now? You have no power against me." He said, his voice having dropped to an almost demonic tone.

"Well, I may not have any powers…" Puzzlehunt said as he kicked a rock that was made by the rubble of the walls. It hit Mystery directly in the stone that gave him all his powers. All the energy tendrils disappeared, and the controlled ponies dropped to the ground. "But I'm still very resourceful." He ran out of the room, after a forlorn glance at Daring Do, and ran up to the roof.

He held up the sonic screwdriver and held it directly to the epicenter of the cloud and turned it on. A hole appeared in the cloud, and the stone that gave him his power, still colored green, fell out right at his hooves. He took a deep breath and reached for it. He had very recently figured out that you'd have to be as crazy as  
Mystery to use it at full capacity. And of course, he was going to need it at full capacity to end this. But he didn't want to end up like his brother. He had to set a point where he could turn back. With little hesitation, he touched the stone.

**=Gaia, Equestria, Baltimare, Baltimare Archeological Institute, Mystery's Office, 1003 C.E. =**

When Mystery's power returned, he was shocked to find that it disappeared just as quickly. The stone was gone from his body. He seethed in anger. He stormed out the office and went to the stairs to the roof. He was fully prepared to kill somepony with his own bare hooves. He climbed the stairs and walked out onto the roof. "Puzzlehunt…"

Suddenly, he was grabbed by the neck, as he the pony who grabbed him leaped the roof and flew directly up.

Puzzlehunt had some occasional lapses in and out of sanity for the next 15 minutes, and he didn't like to think, remember or relive the events of when he was out of it. But lots of things happened to him in life that he didn't like, so every now and he would. He never told anyone the exact details of what happened. All he would say was that the moments he was out were too terrible to think about, and even the moments when he was sane told a pretty terrible story to their very own extent. But, I will tell you a few of the events that happened in those 15 minutes.

As Puzzlehunt flew upwards with Mystery in tow, he beat him up. But that's not all. With every punch, he grew in size. By the time he had reached the end of the upper atmosphere, he had turned into an alicorn with glowing white-hot eyes about the size of Princess Luna, and it was still happening. He was far bigger than Princess Celestia by the time they had flown out of the solar system.

If you're wondering why they hadn't run out of air yet, it's because Puzzlehunt had full unicorn power back again, so he had cast an air shield around them. He had no intention of stopping as he continued beating his hooves into Mystery. With every punch, he allowed himself to be more and more taken over by the stone. He was past the point of being able to stop. He didn't truly want to stop.

Yet somehow, just between his galaxy and the other galaxy nearby, he did stop. He looked down at Mystery. He had been beaten to a pulp, very nearly. He couldn't do this! He had his own will, and you weren't allowed to just ignore that. And so he flew back into his own galaxy. He looked down at Mystery. He wondered what to do with him.

"Well what do I do with you?" He asked.

Mystery couldn't answer.

Puzzlehunt spied a nearby jungle planet. "Well that looks fully hospitable for life." He noted. And with that, he teleported Mystery down to the planet below. He was fairly certain nopony would miss him. He was sure he would be able to adapt fairly quickly to the jungle down there. He might well end up being happy. He wasn't sure if he deserved to be happy, but that wasn't quite his decision to make. He looked around. He deserved to be happy. He had had a very rough life under the near dictatorship of his brother, and he deserved something to get better. He looked at the stone in his chest.

This was not it. He grabbed the stone out of his chest. The air shield around him was designed to work for about 3 minutes after it wasn't being cast. He looked at the stone. An almost evil grin crossed his face. He tore about 20% off of the stone and placed it back in. He looked at the rest of it and tossed it away. It hit a nearby star and burned up into nothing.

Then he turned in the direction of his home planet. He shot a restoration spell at a level to make the whole planet not covered in rubble. It would take 2 days for it to get there. He wondered if he could beat it there. Of course he could! He was pretty amazing! And so, he began moving through space at a motion like he was swimming at high speeds on the path back to Equestria.


	9. Chapter 8: The End of Tomorrow

Chapter 8: The End of Tomorrow

**=Gaia, Equestria, Baltimare, Baltimare Archeological Institute, The Remains of Mystery's Office, 1003 C.E. =**

"So, that's pretty much the entire story." Puzzlehunt finished.

"Hmm. That was certainly pretty…cool, I would think." Daring Do said.

"Yep. And I did it all single hoofedly." Puzzlehunt said.

"But still, when I asked where the Doctor was, why didn't you just go ahead and tell me?" she asked him.

"It would've made the story less dramatic. Don't you know anything about telling stories?" Puzzlehunt said like it was the most obvious thing in the entire world.

Daring Do rubbed her temple with one hoof.

"Okay. I'm guessing the 2 days to the planet looking normal again hasn't hit yet?" Daring Do asked.

"Oh. Well, we've got about…3 minutes." Puzzlehunt said. "Well, that's not good."

"Why not?" she asked.

"Not even enough time to explain scientifically." He said.

Suddenly, the TARDIS materialized, and the Doctor stepped. "Hello-"

"Ah good, you got here just in time! Let's cram ourselves in here!" Puzzlehunt said rapidly as he ran into the TARDIS.

Daring Do snickered a bit and walked into the TARDIS after him.

Puzzlehunt looked surprised, but when he saw the others coming in, he did a terrible attempt to hide it. Daring Do almost laughed at how pathetic it looked. "So, you've been gone awhile." He said.

"I would have been back earlier, if I had actually had my sonic screwdriver." The Doctor said, slightly annoyed.

Puzzlehunt sheepishly handed the dead sonic screwdriver back to him.

"Now, as I was saying, I had prepared all the equipment to make sure you wouldn't die horribly."

"Is that likely to happen?" Puzzlehunt said, trying to maintain his cool as his ears drooped to the side of his head.

"Well, just in case…" The Doctor said.

"You know, I don't exactly think this is necessary!" Puzzlehunt yelled.

The Doctor had strapped him down to a table and restrained all his hooves.

"I don't want you to struggle when this starts to hurt!" The Doctor said back as he pulled out what looked like what barbers use to cut hair, except with three long blades at the very end. "Now I just stick it right here." He said, gesturing to the stone in his chest. "As quickly and violently as I can."

"You don't have to do that." Puzzlehunt said, his voice cracking in terror.

The Doctor didn't reply, he just raised the thing up.

Romana and Daring Do could hear pained screaming all the way in the console room.

"Okay." Puzzlehunt said weakly. "I think I can see blood at the moment, but that wasn't as bad as I thought."

"You get I haven't even started yet, right."

Puzzlehunt's pupils shrank drastically in size.

2 minutes later, The Doctor undid the straps. "Okay, now I'm done."

Puzzlehunt looked at where the stone was, only to find it was gone, yet he still had a horn.

"Yes, all I did was mix it into your genetic structure. Full natural unicorn now." The Doctor said.

Puzzlehunt got up and walked out of the room and out the main doors.

By this point, the recreation spell had hit. The office was fully rebuilt, and the whole world was back to a flourishing order. All of them looked at it happily.

"You know, the worst part is, nopony at all is going to remember that I saved the world." Puzzlehunt said.

Daring Do just groaned.

"So what about your brother?" Romana asked.

"Oh, I'm sure nopony is going to miss him. I'm sure a scandal about how he had been stealing other ponies' discoveries (It's me, I'm talking about myself) will get him fire and somepony else will get this office (Talking about me again)."

"Well, goodbye." The Doctor said.

"Goodbye Doctor. I'm sure things will get better around here." Puzzlehunt said.

"Thanks to our help?" Romana asked hopefully.

"Are you kidding? You were useless during all this!" Puzzlehunt said.

The Doctor sighed and walked back into the TARDIS. Romana and Daring Do soon followed, and the TARDIS dematerialized.

"So, I wonder what the power source Puzzlehunt found actually was?" Romana asked.

"I found out. Do you remember the Entity?" The Doctor asked.

"Rather hard to forget, actually." Daring Do said.

"Well, apparently he's been leaving these little shards across history that feed off things and give them power. I noticed it a short time ago. This particular one was so powerful because it's been around since the dawn of the pony race. It's the big one, so to speak." The Doctor explained

"Couldn't that potentially disrupt pony evolution?" Romana asked.

"I suppose someone needs to figure out." The Doctor said as he began to plot the course. "Lets go!"

**=Gaia, Equestria, Canterlot, Canterlot Royal Archives, Just Outside the Star Swirl the Bearded Wing, 1003 C.E. =**

A Royal Guard member was positioned outside the door to the archive wing, remaining ever vigilant for any intruders.

Suddenly he noticed a pony wearing a cream colored hat with a red band around it. He had his head down so you couldn't see his face.

"Do you have any authorization to be here?" The Guard said. Suddenly, his eyes flashed a golden color.

"Yes I do. Now let me in there." The Guard nodded and put the key in the keyhole

"You know what, why don't you just give me the key." The Guard complied.

"Now how about you go guard that hallway over there and forget the last 10 minutes." The Guard walked away.

Puzzlehunt raised his head and smiled. He turned the key and opened the door. He looked out the window in the direction of the planet where he had left his brother, all those thousands of light years away.

For a second, he could see the planet. Like it was right there as close as the Moon, if not closer.

He ignored it and walked into the room.

To be continued in Episode 6.

But that last part to be continued even later than that.


End file.
